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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
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<html> <head> <title>MayaChemTools:Code:Fingerprints::EStateIndiciesFingerprints.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-Fingerprints::EStateIndiciesFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::EStateIndiciesFingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: EStateIndiciesFingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> 5 <span class="c"># $Revision: 1.19 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span> 40 41 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 42 43 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> 44 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 45 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 46 47 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 48 49 <span class="c"># Setup class variables...</span> 50 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 51 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 52 53 <span class="c"># Overload Perl functions...</span> 54 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyEStateIndiciesFingerprints'</span><span class="sc">;</span> 55 56 <span class="c"># Class constructor...</span> <a name="new-"></a> 57 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 58 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 59 60 <span class="c"># Initialize object...</span> 61 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 62 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> 63 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 64 65 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 66 67 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 68 <span class="s">}</span> 69 70 <span class="c"># Initialize object data...</span> 71 <span class="c">#</span> <a name="_InitializeEStateIndiciesFingerprints-"></a> 72 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprints</span> <span class="s">{</span> 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 74 75 <span class="c"># EStateIndicies is a vector containing sum of E-state values for E-state atom types</span> 76 <span class="c">#</span> 77 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'EStateIndicies'</span><span class="sc">;</span> 78 79 <span class="c"># EStateAtomTypesSetToUse for EStateIndicies:</span> 80 <span class="c">#</span> 81 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span> 82 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined [ Ref 77 ]</span> 83 <span class="c">#</span> 84 <span class="c"># The default EStateAtomTypesSetToUse value for EStateIndicies fingerprints type: ArbitrarySize.</span> 85 <span class="c"># Possible values: ArbitrarySize or FixedSize.</span> 86 <span class="c">#</span> 87 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">''</span><span class="sc">;</span> 88 89 <span class="c"># Assigned E-state atom types...</span> 90 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 91 92 <span class="c"># Vector values precision for real values during E-state indicies...</span> 93 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">3</span><span class="sc">;</span> 94 95 <span class="c"># Calculated E-state values and indicies for generating E-state indicies fingerprints...</span> 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 97 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 98 <span class="s">}</span> 99 100 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 101 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 102 <span class="c">#Class name...</span> 103 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 104 105 <span class="s">}</span> 106 107 <span class="c"># Initialize object properties....</span> <a name="_InitializeEStateIndiciesFingerprintsProperties-"></a> 108 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprintsProperties</span> <span class="s">{</span> 109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 110 111 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> 112 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 113 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 114 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 115 <span class="s">}</span> 116 117 <span class="c"># Make sure molecule object was specified...</span> 118 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 119 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> 120 <span class="s">}</span> 121 122 <span class="i">$This</span><span class="i">->_InitializeEstateIndicies</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 123 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 125 <span class="s">}</span> 126 127 <span class="c"># Initialize E-state indicies...</span> 128 <span class="c">#</span> <a name="_InitializeEstateIndicies-"></a> 129 <span class="k">sub </span><span class="m">_InitializeEstateIndicies</span> <span class="s">{</span> 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 131 132 <span class="c"># Set default EStateAtomTypesSetToUse...</span> 133 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span> 134 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> 135 <span class="s">}</span> 136 137 <span class="c"># Vector type...</span> 138 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 139 140 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> 141 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> 142 <span class="s">}</span> 143 <span class="k">else</span> <span class="s">{</span> 144 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> 145 <span class="s">}</span> 146 147 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 148 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 150 <span class="s">}</span> 151 152 <span class="c"># Disable set size method...</span> 153 <span class="c">#</span> <a name="SetSize-"></a> 154 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span> 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 156 157 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Can't change size: It's not allowed..."</span><span class="sc">;</span> 158 <span class="s">}</span> 159 160 <span class="c"># Set E-state atom types set to use...</span> 161 <span class="c">#</span> <a name="SetEStateAtomTypesSetToUse-"></a> 162 <span class="k">sub </span><span class="m">SetEStateAtomTypesSetToUse</span> <span class="s">{</span> 163 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 164 165 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span> 166 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Can't change size: It's already set..."</span><span class="sc">;</span> 167 <span class="s">}</span> 168 169 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)/i</span><span class="s">)</span> <span class="s">{</span> 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Unknown EStateAtomTypesSetToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> 171 <span class="s">}</span> 172 173 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> 174 175 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 176 <span class="s">}</span> 177 178 <span class="c"># Set vector values precision for real values for E-state indicies...</span> 179 <span class="c">#</span> <a name="SetValuesPrecision-"></a> 180 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span> 181 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 182 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 185 <span class="s">}</span> 186 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> 187 188 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 189 <span class="s">}</span> 190 191 <span class="c"># Generate fingerprints description...</span> 192 <span class="c">#</span> <a name="GetDescription-"></a> 193 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 195 196 <span class="c"># Is description explicity set?</span> 197 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> 198 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> 199 <span class="s">}</span> 200 201 <span class="c"># Generate fingerprints description...</span> 202 203 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span> 204 <span class="s">}</span> 205 206 <span class="c"># Generate electrotopological state indicies (E-state) [ Ref 75-78 ] fingerprints for</span> 207 <span class="c"># non-hydrogen atoms in a molecule...</span> 208 <span class="c">#</span> 209 <span class="c"># EStateIndicies fingerprints constitute a vector containing sum of E-state values</span> 210 <span class="c"># for E-state atom types. Two types of E-state atom types set size are allowed:</span> 211 <span class="c">#</span> 212 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span> 213 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined</span> 214 <span class="c">#</span> 215 <span class="c"># Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to</span> 216 <span class="c"># non-hydrogen atoms in the molecule which is able to assign atom types to any valid</span> 217 <span class="c"># atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed</span> 218 <span class="c"># set of E-state atom types corresponding to specific atom groups [ Appendix III in</span> 219 <span class="c"># Ref 77 ] are used for fingerprints.</span> 220 <span class="c">#</span> 221 <span class="c"># The fixed size E-state atom type set size used during generation of fingerprints corresponding</span> 222 <span class="c"># FixedSize value of EStateAtomTypesSetToUse contains 87 E-state non-hydrogen atom types</span> 223 <span class="c"># in EStateAtomTypes.csv data file distributed with MayaChemTools.</span> 224 <span class="c">#</span> 225 <span class="c"># Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of</span> 226 <span class="c"># E-state indicies fingerprints:</span> 227 <span class="c">#</span> 228 <span class="c"># Type EStateAtomTypesSetToUse</span> 229 <span class="c">#</span> 230 <span class="c"># EStateIndicies ArbitrarySize [ default fingerprints ]</span> 231 <span class="c"># EStateIndicies FixedSize</span> 232 <span class="c">#</span> 233 <span class="c"># The default is generate EStateIndicies type fingeprints corresponding to ArbitrarySize as</span> 234 <span class="c"># EStateAtomTypesSetToUse value.</span> 235 <span class="c">#</span> 236 <span class="c">#</span> <a name="GenerateFingerprints-"></a> 237 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 239 240 <span class="c"># Cache appropriate molecule data...</span> 241 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 242 243 <span class="c"># Assign E-state atom types...</span> 244 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignEStateAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 245 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't assign valid E-state atom types to all atoms..."</span><span class="sc">;</span> 246 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 247 <span class="s">}</span> 248 249 <span class="c"># Calculate E-state indicies...</span> 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateIndicies</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 251 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't calculate E-state values for all atoms..."</span><span class="sc">;</span> 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 253 <span class="s">}</span> 254 255 <span class="c"># Set final fingerprints...</span> 256 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 257 258 <span class="c"># Clear cached molecule data...</span> 259 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 260 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 262 <span class="s">}</span> 263 264 <span class="c"># Assign E-state atom types...</span> 265 <span class="c">#</span> <a name="_AssignEStateAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignEStateAtomTypes</span> <span class="s">{</span> 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 268 <span class="k">my</span><span class="s">(</span><span class="i">$EStateAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span> 269 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 271 272 <span class="c"># Assign E-state atom types...</span> 273 <span class="i">$EStateAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 274 <span class="i">$EStateAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 275 276 <span class="c"># Make sure atom types assignment is successful...</span> 277 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 278 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 279 <span class="s">}</span> 280 281 <span class="c"># Collect assigned atom types...</span> 282 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 283 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 284 285 <span class="i">$AtomType</span> = <span class="i">$EStateAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 286 <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomType</span><span class="sc">;</span> 287 <span class="s">}</span> 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 289 <span class="s">}</span> 290 291 <span class="c"># Calculate E-state indicies by summing up E-state values for specific</span> 292 <span class="c"># E-state atom types...</span> 293 <span class="c">#</span> <a name="_CalculateEStateIndicies-"></a> 294 <span class="k">sub </span><span class="m">_CalculateEStateIndicies</span> <span class="s">{</span> 295 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 296 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span> 297 298 <span class="c"># Calculate E-state values to generate E-state indicies...</span> 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 300 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 301 <span class="s">}</span> 302 303 <span class="c"># Calculate E-state indicies...</span> 304 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 305 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 306 307 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 308 <span class="i">$EStateValue</span> = <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 309 310 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> 311 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span> 312 <span class="s">}</span> 313 314 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} += <span class="i">$EStateValue</span><span class="sc">;</span> 315 <span class="s">}</span> 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 317 <span class="s">}</span> 318 319 <span class="c"># Calculate E-state values for E-state indicies...</span> 320 <span class="c">#</span> <a name="_CalculateEStateValuesDescriptors-"></a> 321 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span> 322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 323 <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span> 324 325 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 326 327 <span class="c"># Calculate and assign E-state values...</span> 328 <span class="i">$EStateValuesDescriptors</span> = <span class="i">new</span> <span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 329 <span class="i">$EStateValuesDescriptors</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 330 331 <span class="c"># Make sure E-state values calculation is successful...</span> 332 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateValuesDescriptors</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 333 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 334 <span class="s">}</span> 335 336 <span class="c"># Collect assigned E-state values...</span> 337 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 338 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 339 <span class="i">$EStateValue</span> = <span class="i">$EStateValuesDescriptors</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 340 <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span> 341 <span class="s">}</span> 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 343 <span class="s">}</span> 344 345 <span class="c"># Set final final fingerpritns for E-state indicies...</span> 346 <span class="c">#</span> <a name="_SetFinalFingerprints-"></a> 347 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> 348 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 349 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$EStateAtomTypesDataRef</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> 350 351 <span class="c"># Mark successful generation of fingerprints...</span> 352 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 353 354 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 355 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 356 357 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span> 358 359 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> 360 <span class="c"># Use fixed size E-state atom types set for non-hydrogen atoms...</span> 361 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 362 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span> 363 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> ? <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 364 <span class="s">}</span> 365 <span class="s">}</span> 366 <span class="k">else</span> <span class="s">{</span> 367 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}}<span class="s">)</span> <span class="s">{</span> 368 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span> 369 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span><span class="sc">;</span> 370 <span class="s">}</span> 371 <span class="s">}</span> 372 373 <span class="c"># Add IDs and values to fingerprint vector...</span> 374 <span class="k">if</span> <span class="s">(</span><span class="i">@IDs</span><span class="s">)</span> <span class="s">{</span> 375 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> 376 <span class="s">}</span> 377 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> 378 379 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 380 <span class="s">}</span> 381 382 <span class="c"># Cache appropriate molecule data...</span> 383 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 384 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 385 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 386 387 <span class="c"># Get all non-hydrogen atoms...</span> 388 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 389 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> 390 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 391 392 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 393 <span class="s">}</span> 394 395 <span class="c"># Clear cached molecule data...</span> 396 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 397 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 399 400 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 401 402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 403 <span class="s">}</span> 404 405 <span class="c"># Return a string containg data for EStateIndiciesFingerprints object...</span> <a name="StringifyEStateIndiciesFingerprints-"></a> 406 <span class="k">sub </span><span class="m">StringifyEStateIndiciesFingerprints</span> <span class="s">{</span> 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 408 <span class="k">my</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprintsString</span><span class="s">)</span><span class="sc">;</span> 409 410 <span class="c"># Type of Keys...</span> 411 <span class="i">$EStateIndiciesFingerprintsString</span> = <span class="q">"Type: $This->{Type}; EStateAtomTypesSetToUse: $This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span> 412 413 <span class="c"># Fingerprint vector...</span> 414 <span class="i">$EStateIndiciesFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> 415 416 <span class="k">return</span> <span class="i">$EStateIndiciesFingerprintsString</span><span class="sc">;</span> 417 <span class="s">}</span> 418 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>